External Email - Use Caution Thank you very much for your quick response. I still have a challenge locating the output file after running the suggested command ( mri_cnr $SUBJECTS_DIR/bert/surf/ $SUBJECTS_DIR/bert/mri/norm.mgz) with my subject. Can you please provide me with the full command for calculating contrast-to-noise ratio and signal-to-noise ratio of white matter, gray matter and CSF since am a beginner Or a video link to calculate them.
This is what i see after running the command mri_cnr /Applications/freesurfer/7.1.1/SUBNEW/PA1//label/lh.cortex.label mri_cnr -- compute the gray/white/csf contrast-to-noise ratio for volumes. usage: mri_cnr [options] <surf directory> <vol 1> <vol 2> ... usage example (assumes fs pipeline has finished for subject subj1): mri_cnr subj1/surf subj1/mri/orig.mgz Available options: -s <slope_fname> <dist in> <dist out> <step in> <step out>: compute slope based on given values, write it to slope and offset files labeled <slope_fname> (e.g., `lh.<slope_fname>.slope.mgz') -t : print only the total CNR to stdout (stderr still contains more information) -l <logfile>: log cnr to file <logfile>. Will contain 8 values in the following order: gray_white_cnr, gray_csf_cnr, white_mean, gray_mean, csf_mean, sqrt(white_var), sqrt(gray_var), sqrt(csf_var) label <lh> <rh>: read hemisphere labels from <lh> and <rh> -u, -?, -help : print usage information and quit -version : print software version information and quit. On Thu, Feb 9, 2023 at 3:46 PM John Anderson <jb19790...@gmail.com> wrote: > External Email - Use Caution > > You might consider the command wm-anat-snr to compute SNR > > On Thu, Feb 9, 2023 at 10:38 AM Kumar, Avnish < > avnish.ku...@mgh.harvard.edu> wrote: > >> You could also use these: >> >> 1. For CNR you can use the mri_cnr tool: >> >> mri_cnr [options] <surf directory> <vol 1> >> >> For example: >> >> mri_cnr $SUBJECTS_DIR/bert/surf/ $SUBJECTS_DIR/bert/mri/norm.mgz >> >> >> >> 1. For SNR, you'll have to calculate them as: >> 1. >> >> Run the recon-all pipeline to process your MRI data. >> 2. >> >> Use the mri_binarize tool to create a binary mask of the ROI in >> the image. >> 3. >> >> Use the mri_segstats tool to calculate the mean and standard >> deviation of the intensity values within the ROI. >> 4. >> >> Then your SNR = mean_intensity/std_of_intensity. >> >> >> Best, >> >> Avnish >> ------------------------------ >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing < >> yhuan...@mgh.harvard.edu> >> *Sent:* Tuesday, February 7, 2023 9:09 AM >> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> *Subject:* Re: [Freesurfer] MRI image quality metrics >> >> >> Hi, >> >> >> >> The following is taken from *MailScanner has detected a possible fraud >> attempt from "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1yBb2GkovBSvAi4q4ORDMfb9gbA5D1lxhgbEGgbhkKPLCst71OzbiO7rlTXt6C6Wbg0iqueaHjfQM9_qum2y_-Y4u_C4WRrtG3dCaj3nM3_VYSuuF2eAWlqATUXQWw_xWGDFx5AAjuJPXZki7FqWWBTiadsDRipZu4deosCGVqBDkMdoRPo563fpbTTDXHISB8J6cHn1vqSjOpZScG5d3rHsfpwyO-0jRIVnkUhDElQfYL1Bq3_zQLNLxPppkBtR_vY_9AFghhGXw63wfZTo1ljfMKva5j-7Ghq1B6-girB3pGRPj-6lwiOSuUXUBNyCy2XUlPfL2G6qfdbnc4_hKjMqOfEUiGIsb1_pk4d5Rdmo/https%3A%2F%2Fgithub.com%2FComaRecoveryLab%2FLesion_Correction >> <https://secure-web.cisco.com/1thfo9hWCJUK_nYfNM9axD5kjhrzv1nVC_cWmWT2aic2ttFqLtKhuhi9E6AA5fXRqlBpbp24-HV_sfbVQik2RJDyE7c9eALg8zbpl340Dwhl2aijQIJcCFqj9K_RZhk5xCVRHURT36bgdsm5C36VxQ3fQh7sVLpsmxKo0Ie0hB8HrgI8Rn7JySIK5iCJZWL9q1OqnFWJgdRUgMDrVlJVf356x-vM1sz0IWVGsGErBQNdxLAYcSvFCTWx0fb6tb1mCw7ljDzERXM7qU-fnbvpV-AKWSuj0eVKouZoNRp8SgTUOIA2mR_VbqAJw9K2PU4OKa4g3f30QsCJpd0U1hcNz7Q/https%3A%2F%2Fgithub.com%2FComaRecoveryLab%2FLesion_Correction> >> as mentioned in this paper *MailScanner has detected a possible fraud >> attempt from "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1xSgxlzAik8YTDjWAB7qFryOCtl3ASznPC5ZYb3rUdYk5SxbDkBbMuYef3EnJjxEssoeDeEjiupNTkDirzIc3qiJi4ux16RvcF7tycU_BdmfIXAoEAiv4bN66PV4pD0LPUXHgHd4kkDuOkjOclxBUA2sqnMGd6XtSMpEy5ZP_TRgTFMDSy3haj-XcLFe8QJ_22E_7GqKsuKPcUzl5y6DbF_hSzb1mCGWT-NsnqB5NeTpvg6cTrvbzryiAAVvHACLNLTVJsu1XICCxfJexxi0l14kmNvFJJQTnpHQ543zbasyUHlBwULVvn7eTSRJsJcVh6dyznGfyxe1R3nMjHptqrhr8TvyqLfKrmiNYzMknqxQ/https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS2215016120302144 >> <https://secure-web.cisco.com/1aMzZKpIcKTLwbYP_79ZqCUH8p9h0Xh4xqpm8fsmVREKN8hATdl6DHCSkFDKqidqmKqoAydr5eDqjVLAQDKN0zmR2k2Wckx-sv1P3JgKJVQWfpIVeyrh0tqwnGzqQm3nK9BQGA7rUSYwaCBBjmogAhlrnepeAo1_J0CQXj4rKMM-V_g9sXIIirV1h-sajPjULI9qcQw2orS-vs9tl65xAbfrEtmtZ35-IZO43Wk-1D2CsVkFyKCsuGxT5qcGTg9FV3VSUbHpeA-dKS1qkv8zYKtz4i-JeRm0y4E6YAs_B91ccue5fFsCAMyN4jKTPxkhNk7f7IRaIrbfA6GYyWFCX7A/https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS2215016120302144> >> >> >> >> “ >> >> Qualitative and Quantitative Assessment of MRI Data >> >> >> >> SNR: We calculated SNR for each subject using the “wm-anat-snr” >> FreeSurfer tool available in FreeSurfer v6.0. Voxels from the subject’s >> normalized T1 (norm.mgz) that containing white matter (WM) as defined by >> the subject’s aparc+aseg.mgz are used to calculate SNR with this tool. >> >> >> >> SNR = (mean WM)/(stdev WM) >> >> >> >> We ran the following command for each subject: >> >> >> >> wm-anat-snr –s >> >> >> >> CNR: We calculated CNR for each subject using the “mri_cnr” FreeSurfer >> tool available in FreeSurfer v6.0. This tool finds the average between two >> CNRs: the subject’s (1) WM and gray matter (GM) CNR and (2) gray matter and >> cerebrospinal fluid (CSF) CNR. The average CNR is then calculated and >> reported for each hemisphere. Finally, the CNR for both hemispheres are >> averaged to produce a full brain CNR. >> >> >> >> WM-GM CNR = (delta(WM,GM)^2)/(total variance) GM-CSF CNR = >> (delta(GM,CSF)^2)/(total variance) Hemisphere CNR = (WM-GM CNR + GM-CSF >> CNR) x 2 Full Brain CNR = (Left Hemisphere CNR + Right Hemisphere CNR) x 2 >> >> “ >> >> >> >> >> >> Best, >> >> >> >> Yujing >> >> >> >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *MANSON ERIC NAAB >> *Sent:* Tuesday, February 7, 2023 5:26 AM >> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> *Subject:* [Freesurfer] MRI image quality metrics >> >> >> >> * External Email - Use Caution * >> >> Dear FreeSurfer experts, >> >> Please, I need your assistance and guidance on calculating the >> contrast-to-noise ratio (CNR) and signal-to-noise-ratio (SNR) of White >> matter, Gray matter, and CSF of the brain after recon-all. >> >> >> >> Thank you >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1ZggDbPTzdGw9n6UPfbx6DkxHs3xPFi3eKXLAAkQkDTA-uqYQfKl65cTTB3g3_XKyrnBHR3Zw1eDjbO2HCs5qmTjlUq4xWVSbnclwdQQph0VClYXh56USHneE6qaAB3c-oacMn61HmljzBznua2NJf2wXlaZ0RtPb3YXh9qWy9uER7kr-0TUsO5VcTrXRVbyIlQGZhavytsQXByK1zrGINyHgpzAGc7dPd9Vtj2C2SJTVU-7DwQMg6G0Kuqidk9OrzWZi6jTXMSHWp77ZYy2UHUShbEwdf1Nok34ILyVyQHJz1ftIrzRQiYjibEXyMUDczPSinX9bvPi9MhQfHhYurx_i2MHYBEetOZm-eN9tdKM/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1KDvbAKLrFBoPVGyqH2wpBHTCZi4G5JP4CoyRC23fpSgjgmUjIEIDk5ijfEjY7EcdqD7NMLPnurOJaIh0CESkCjdM-kajpNjDkBcmErgdRD0D7VHpAkbJK2Z0vtuzM98dlYvFfoA5RP_t9tAeeRdA-qZEqMyVFnCZytNMwGX7C6SXBJqlptH_9ue8D3YojwI-o03MasVSWHISnuBb-vLjFPQCtTLtRx7VahTcU3GnkMyiIRc3tk2mxwZDkdAvRHcODMGxX35AEUnYGnF7jDNZBlV8elaazdpSJr7VfItSdTLokLwsLxycodEFhQVZk1M8fBPC2gWDxUKYUo3Ku9AgQg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> The information in this e-mail is intended only for the person to whom it >> is addressed. 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